Structure Menu in MarvinSketch

This menu provides chemical functions relating to structures like molecule cleaning, aromatization, reaction-handling, naming, and more.

Menu item

Icon

Description

Clean 2D > Clean in 2D

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Calculates new 2D coordinates for the molecule.

Clean 2D > Clean and Arrange in 2D

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Cleans structures and positions them to the center of the canvas.

Clean 2D > Hydrogenize Chiral Center

N/A

Adds an explicit hydrogen atom to a chiral center having no terminal atoms when 2D cleaning is performed.

Clean 3D

images/download/attachments/1805322/clean_3d24.png

Calculates 3D coordinates for the molecule base on the method set in the Preferences > 3D Options dialog.

Directed Merge > Assign Atoms

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Chooses the atoms of the fragments to be merged.

Directed Merge > Merge

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Merges the fragments at the atoms set.

Add > Add Explicit Hydrogens

images/download/thumbnails/1805322/hydrogenize24.png

Adds explicit H atoms instead of the current implicit ones. Explicit hydrogens are displayed with atoms joining their neighbor while implicit hydrogens are displayed by atom symbols only.

Add > Data

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Attaches data such as the stoichiometry coefficient to the molecule.

Add > Absolute Stereo (CHIRAL)

images/download/thumbnails/1805322/absolute_stereo24.png

Sets chiral flag for the molecule.

Add > Multi-Center

N/A

Adds a multi-center attachment point representing a group of atoms.

Add > Position Variation Bond

images/download/thumbnails/1805634/markushbond24.png

Create a variable point of attachment to represent a connection point to a group of atoms.

Add > No Structure

N/A

Places a No Structure label on the canvas.

Remove > Explicit Hydrogens

images/download/thumbnails/1805322/dehydrogenize24.png

Removes explicit H atoms and increases the number of implicit hydrogens.

Remove > Data

N/A

Removes the attached data from the molecule.

Remove > Absolute Stereo (CHIRAL)

images/download/thumbnails/1805322/remove_absolute_stereo24.png

Removes the chiral flag of the molecule.

Edit data

N/A

Changes a previously attached data such as the stoichiometry coefficient of the molecule.

Edit properties

N/A

Bond properties can be edited from this menu.

Aromatic Form > Convert to Aromatic Form

images/download/thumbnails/1805322/aromatize24.png

Transforms the molecule to aromatic representation using the transformation method set.

Aromatic Form > Conversion Method > Basic

N/A

The basic aromatization method is described here.

Aromatic Form > Conversion Method > General

N/A

The general aromatization method is described here.

Aromatic Form > Conversion Method > Loose

N/A

The loose aromatization method is described here.

Aromatic Form > Convert to Kekulé Form

images/download/thumbnails/1805322/dearomatize24.png

Transforms the molecule to non-aromatic representation.

Group > Group

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Creates a custom Substructure Group (S-group).

Group > Frequency Variation

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Creates a Repeating Unit with Repetition Ranges.

Group > Merge Brackets

N/A

Creates a bracket that crosses two bonds.

Group > Edit Group

N/A

Modifies the properties of the selected group.

Group > Contract Group

N/A

Contracts all groups to their abbreviations.

Group > Expand Group

N/A

Displays the full structure instead of the abbreviations.

Group > Ungroup

N/A

Removes all abbreviated group associations from the molecule.

Reaction > Merge Reactants

N/A

Merges the selected fragments to a reactant, product, or agent.

Reaction > Unmerge Reactants

N/A

Removes selected fragments from a previously merged reactant, product, or agent.

Mapping > Map Atoms

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Inserts map numbers of the selected atoms.

Mapping > Manual Atom Map

images/download/thumbnails/1805683/map4b.png

Inserts map numbers manually.

Mapping > Reaction Mapping Method > Complete

N/A

All atoms in the reaction are mapped.

Mapping > Reaction Mapping Method > Changing

N/A

Only those atoms are mapped that have changing bond. Either the bond order changes, a new bond is created, or the bond is deleted. Orphan and widow atoms are included.

Mapping > Reaction Mapping Method > Matching

N/A

Maps all matching atoms in the reaction (Daylight style mapping). A reaction atom is called matching if it is not an orphan/widow atom: it exists on both sides of the reaction.

Mapping > Unmap Atoms

images/download/thumbnails/1805322/unmap_reaction24.png

Removes map numbers of the selected atoms.

R-Logic

N/A

Allows setting additional R-group conditions such as occurrence, rest H, and if-then expressions to R-groups in the R-logic dialog window.

Place Analysis Box

N/A

Places the Analysis Box containing the preset calculations.

Structure to Name

N/A

Generates IUPAC and/or Traditional Name and/or displays CAS Registry Numbers®.

Name to Structure

N/A

Opens the Source window in IUPAC Name format, and enables you to enter directly an IUPAC Name and convert it to structure.

Markush Enumeration

N/A

Generates a whole or a subset of the library of a generic Markush Structure.

Check Structure

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Checks and corrects chemical structures. See Structure Checker for more information.

Auto Check

N/A

Toggles auto checking of structures while drawing.